PhyloDat’AIDS

At a glance

Sequence database

This dataset include 18,708 unique individuals.

Time points

Sampling period

Monthly

Yearly

Regions covered

at a glance

pol (PR/RT and integrase)

Sensitivity analyses to evaluate number of individuals by minimum sequencing length.

PR/RT

Sensitivity analyses to evaluate number of individuals by minimum sequencing length.

Demographics

Below I am showing the data from the 13538 participants with a minimum length og 500 bp PR/RT covering PR/RT.

Characteristic N = 13,5381
sex
    Female 4,034 (30%)
    Male 9,392 (69%)
    Transgender F/M 2 (<0.1%)
    Transgender M/F 110 (0.8%)
Age 51 (40, 59)
Age group
    <15 0 (0%)
    ≥15-<25 351 (2.6%)
    ≥25-<35 1,699 (13%)
    ≥35-<45 2,759 (20%)
    ≥45-<55 3,402 (25%)
    ≥55-<80 5,154 (38%)
    ≥80 173 (1.3%)
WHO region (origin)
    WHO Africa 2,445 (20%)
    WHO Americas 725 (5.9%)
    WHO Eastern Mediterranean 283 (2.3%)
    WHO Europe 8,684 (71%)
    WHO South-East Asia 43 (0.4%)
    WHO Western Pacific 72 (0.6%)
Regions francaises
    Auvergne-Rhône-Alpes 303 (2.2%)
    Bourgogne-Franche-Comté 18 (0.1%)
    Bretagne 1,256 (9.3%)
    Centre-Val de Loire 26 (0.2%)
    Corse 34 (0.3%)
    Grand Est 12 (<0.1%)
    Guadeloupe 645 (4.8%)
    Guyane française 8 (<0.1%)
    Hauts-de-France 29 (0.2%)
    Île-de-France 160 (1.2%)
    Martinique 922 (6.8%)
    Mayotte 1 (<0.1%)
    Normandie 690 (5.1%)
    Nouvelle-Aquitaine 154 (1.1%)
    Occitanie 3,626 (27%)
    Pays de la Loire 2,863 (21%)
    Provence-Alpes-Côte-d'Azur 2,787 (21%)
    Réunion 4 (<0.1%)
HIV stage
    A 8 (<0.1%)
    A0 31 (0.2%)
    A1 1,650 (12%)
    A2 4,521 (33%)
    A3 2,526 (19%)
    B 2 (<0.1%)
    B0 20 (0.1%)
    B1 102 (0.8%)
    B2 608 (4.5%)
    B3 909 (6.7%)
    C 35 (0.3%)
    C0 10 (<0.1%)
    C1 65 (0.5%)
    C2 429 (3.2%)
    C3 2,622 (19%)
Primo-infection
    Non 12,295 (91%)
    Oui 1,243 (9.2%)
Transmission risk
    Bisexual 737 (5.4%)
    Blood 237 (1.8%)
    Heterosexual 5,786 (43%)
    IDU 887 (6.6%)
    Mother to child transmission 221 (1.6%)
    MSM 5,028 (37%)
    Others 81 (0.6%)
    Unknown 561 (4.1%)
Drug use
    Current 1,228 (10%)
    None 6,765 (56%)
    Past 1,310 (11%)
    Sometimes 575 (4.7%)
    Substitution 180 (1.5%)
    Unknown 2,118 (17%)
Baseline HIV RNA level (log10) 4.80 (4.11, 5.44)
Baseline CD4 count 380 (203, 572)
1 n (%); Median (IQR)

Geospatial distribution

Sampling by region

All territories with background

All territories without background

France (mainland)

Global Network analyses

Cluster start date is defined as join date when the 3rd participant joins clusters. Not terribly important in our analysis, more important in time-to-event analyses.

\[ NormalizedClusterGrowth_{PastYear} = \frac{{ClusterGrowth}_{PastYear}}{\sqrt{ClusterSize}_{PastYear}} \]

To account for the size of the cluster, I normalized cluster growth by the square root of cluster size. For example, the cluster size for a given cluster in the past year is the size of the cluster at the beginning of the year, before any any have been added.

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 2,295/13,538, i.e. 17%.

Cluster size and composition

Overall

By dispersal

Demographics by clustering status

Characteristic Overall, N = 13,5381 Clusters size ≥3, N = 1,3631 Singletons, N = 12,1751 p-value2
sex


<0.001
    Female 4,034 (30%) 107 (7.9%) 3,927 (32%)
    Male 9,392 (69%) 1,247 (91%) 8,145 (67%)
    Transgender F/M 2 (<0.1%) 0 (0%) 2 (<0.1%)
    Transgender M/F 110 (0.8%) 9 (0.7%) 101 (0.8%)
Age 51 (40, 59) 42 (33, 53) 51 (41, 60) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 351 (2.6%) 68 (5.0%) 283 (2.3%)
    ≥25-<35 1,699 (13%) 313 (23%) 1,386 (11%)
    ≥35-<45 2,759 (20%) 377 (28%) 2,382 (20%)
    ≥45-<55 3,402 (25%) 322 (24%) 3,080 (25%)
    ≥55-<80 5,154 (38%) 275 (20%) 4,879 (40%)
    ≥80 173 (1.3%) 8 (0.6%) 165 (1.4%)
WHO region (origin)



    WHO Africa 2,445 (20%) 61 (4.8%) 2,384 (22%)
    WHO Americas 725 (5.9%) 33 (2.6%) 692 (6.3%)
    WHO Eastern Mediterranean 283 (2.3%) 20 (1.6%) 263 (2.4%)
    WHO Europe 8,684 (71%) 1,150 (91%) 7,534 (69%)
    WHO South-East Asia 43 (0.4%) 1 (<0.1%) 42 (0.4%)
    WHO Western Pacific 72 (0.6%) 2 (0.2%) 70 (0.6%)
Regions francaises



    Auvergne-Rhône-Alpes 303 (2.2%) 23 (1.7%) 280 (2.3%)
    Bourgogne-Franche-Comté 18 (0.1%) 3 (0.2%) 15 (0.1%)
    Bretagne 1,256 (9.3%) 102 (7.5%) 1,154 (9.5%)
    Centre-Val de Loire 26 (0.2%) 4 (0.3%) 22 (0.2%)
    Corse 34 (0.3%) 2 (0.1%) 32 (0.3%)
    Grand Est 12 (<0.1%) 0 (0%) 12 (<0.1%)
    Guadeloupe 645 (4.8%) 47 (3.4%) 598 (4.9%)
    Guyane française 8 (<0.1%) 0 (0%) 8 (<0.1%)
    Hauts-de-France 29 (0.2%) 3 (0.2%) 26 (0.2%)
    Île-de-France 160 (1.2%) 12 (0.9%) 148 (1.2%)
    Martinique 922 (6.8%) 99 (7.3%) 823 (6.8%)
    Mayotte 1 (<0.1%) 0 (0%) 1 (<0.1%)
    Normandie 690 (5.1%) 53 (3.9%) 637 (5.2%)
    Nouvelle-Aquitaine 154 (1.1%) 24 (1.8%) 130 (1.1%)
    Occitanie 3,626 (27%) 428 (31%) 3,198 (26%)
    Pays de la Loire 2,863 (21%) 260 (19%) 2,603 (21%)
    Provence-Alpes-Côte-d'Azur 2,787 (21%) 302 (22%) 2,485 (20%)
    Réunion 4 (<0.1%) 1 (<0.1%) 3 (<0.1%)
HIV stage



    A 8 (<0.1%) 3 (0.2%) 5 (<0.1%)
    A0 31 (0.2%) 4 (0.3%) 27 (0.2%)
    A1 1,650 (12%) 328 (24%) 1,322 (11%)
    A2 4,521 (33%) 646 (47%) 3,875 (32%)
    A3 2,526 (19%) 177 (13%) 2,349 (19%)
    B 2 (<0.1%) 0 (0%) 2 (<0.1%)
    B0 20 (0.1%) 1 (<0.1%) 19 (0.2%)
    B1 102 (0.8%) 13 (1.0%) 89 (0.7%)
    B2 608 (4.5%) 40 (2.9%) 568 (4.7%)
    B3 909 (6.7%) 30 (2.2%) 879 (7.2%)
    C 35 (0.3%) 2 (0.1%) 33 (0.3%)
    C0 10 (<0.1%) 0 (0%) 10 (<0.1%)
    C1 65 (0.5%) 5 (0.4%) 60 (0.5%)
    C2 429 (3.2%) 22 (1.6%) 407 (3.3%)
    C3 2,622 (19%) 92 (6.7%) 2,530 (21%)
Primo-infection


<0.001
    Non 12,295 (91%) 1,042 (76%) 11,253 (92%)
    Oui 1,243 (9.2%) 321 (24%) 922 (7.6%)
Transmission risk


<0.001
    Bisexual 737 (5.4%) 113 (8.3%) 624 (5.1%)
    Blood 237 (1.8%) 12 (0.9%) 225 (1.8%)
    Heterosexual 5,786 (43%) 249 (18%) 5,537 (45%)
    IDU 887 (6.6%) 36 (2.6%) 851 (7.0%)
    Mother to child transmission 221 (1.6%) 1 (<0.1%) 220 (1.8%)
    MSM 5,028 (37%) 918 (67%) 4,110 (34%)
    Others 81 (0.6%) 5 (0.4%) 76 (0.6%)
    Unknown 561 (4.1%) 29 (2.1%) 532 (4.4%)
Drug use


<0.001
    Current 1,228 (10%) 221 (18%) 1,007 (9.2%)
    None 6,765 (56%) 616 (49%) 6,149 (56%)
    Past 1,310 (11%) 135 (11%) 1,175 (11%)
    Sometimes 575 (4.7%) 113 (9.0%) 462 (4.2%)
    Substitution 180 (1.5%) 9 (0.7%) 171 (1.6%)
    Unknown 2,118 (17%) 162 (13%) 1,956 (18%)
Baseline HIV RNA level (log10) 4.80 (4.11, 5.44) 4.95 (4.35, 5.64) 4.78 (4.07, 5.42) <0.001
Baseline CD4 count 380 (203, 572) 475 (324, 651) 362 (180, 556) <0.001
1 n (%); Median (IQR)
2 Fisher’s exact test; Wilcoxon rank sum test; Pearson’s Chi-squared test

Network analyses by region

Pays de la Loire

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 260/2,863, i.e. 9%.

Cluster size and composition

Overall

By origin

Demographics by clustering status

Characteristic Overall, N = 2,8631 Clusters size ≥3, N = 2601 Singletons, N = 2,6031 p-value2
sex


<0.001
    Female 965 (34%) 27 (10%) 938 (36%)
    Male 1,887 (66%) 232 (89%) 1,655 (64%)
    Transgender M/F 11 (0.4%) 1 (0.4%) 10 (0.4%)
Age 51 (41, 60) 47 (38, 56) 51 (41, 60) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 55 (1.9%) 3 (1.2%) 52 (2.0%)
    ≥25-<35 333 (12%) 44 (17%) 289 (11%)
    ≥35-<45 572 (20%) 65 (25%) 507 (19%)
    ≥45-<55 744 (26%) 74 (28%) 670 (26%)
    ≥55-<80 1,131 (40%) 71 (27%) 1,060 (41%)
    ≥80 28 (1.0%) 3 (1.2%) 25 (1.0%)
WHO region (origin)



    WHO Africa 829 (30%) 15 (5.8%) 814 (32%)
    WHO Americas 69 (2.5%) 4 (1.5%) 65 (2.6%)
    WHO Eastern Mediterranean 56 (2.0%) 2 (0.8%) 54 (2.1%)
    WHO Europe 1,821 (65%) 237 (91%) 1,584 (62%)
    WHO South-East Asia 11 (0.4%) 0 (0%) 11 (0.4%)
    WHO Western Pacific 22 (0.8%) 2 (0.8%) 20 (0.8%)
HIV stage



    A 1 (<0.1%) 1 (0.4%) 0 (0%)
    A0 4 (0.1%) 0 (0%) 4 (0.2%)
    A1 267 (9.3%) 39 (15%) 228 (8.8%)
    A2 993 (35%) 127 (49%) 866 (33%)
    A3 624 (22%) 45 (17%) 579 (22%)
    B0 3 (0.1%) 0 (0%) 3 (0.1%)
    B1 11 (0.4%) 1 (0.4%) 10 (0.4%)
    B2 151 (5.3%) 11 (4.2%) 140 (5.4%)
    B3 204 (7.1%) 9 (3.5%) 195 (7.5%)
    C 6 (0.2%) 0 (0%) 6 (0.2%)
    C0 1 (<0.1%) 0 (0%) 1 (<0.1%)
    C1 12 (0.4%) 0 (0%) 12 (0.5%)
    C2 90 (3.1%) 6 (2.3%) 84 (3.2%)
    C3 496 (17%) 21 (8.1%) 475 (18%)
Primo-infection


<0.001
    Non 2,659 (93%) 199 (77%) 2,460 (95%)
    Oui 204 (7.1%) 61 (23%) 143 (5.5%)
Transmission risk



    Bisexual 128 (4.5%) 16 (6.2%) 112 (4.3%)
    Blood 60 (2.1%) 2 (0.8%) 58 (2.2%)
    Heterosexual 1,335 (47%) 53 (20%) 1,282 (49%)
    IDU 141 (4.9%) 4 (1.5%) 137 (5.3%)
    Mother to child transmission 53 (1.9%) 0 (0%) 53 (2.0%)
    MSM 1,039 (36%) 182 (70%) 857 (33%)
    Others 13 (0.5%) 1 (0.4%) 12 (0.5%)
    Unknown 94 (3.3%) 2 (0.8%) 92 (3.5%)
Drug use



    Current 236 (8.6%) 40 (16%) 196 (7.8%)
    None 1,875 (68%) 160 (63%) 1,715 (69%)
    Past 261 (9.5%) 20 (7.8%) 241 (9.7%)
    Sometimes 147 (5.3%) 28 (11%) 119 (4.8%)
    Substitution 26 (0.9%) 2 (0.8%) 24 (1.0%)
    Unknown 207 (7.5%) 5 (2.0%) 202 (8.1%)
Baseline HIV RNA level (log10) 4.80 (4.09, 5.42) 4.87 (4.40, 5.66) 4.77 (4.06, 5.40) <0.001
Baseline CD4 count 366 (190, 558) 438 (317, 612) 348 (175, 551) <0.001
1 n (%); Median (IQR)
2 Fisher’s exact test; Wilcoxon rank sum test; Pearson’s Chi-squared test

Cluster growth

Top growing clusters

New entries

Occitanie

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 353/3,626, i.e. 10%.

Cluster size and composition

Overall

By origin

Demographics by clustering status

Characteristic Overall, N = 3,6261 Clusters size ≥3, N = 3531 Singletons, N = 3,2731 p-value2
sex


<0.001
    Female 898 (25%) 10 (2.8%) 888 (27%)
    Male 2,712 (75%) 340 (96%) 2,372 (72%)
    Transgender M/F 16 (0.4%) 3 (0.8%) 13 (0.4%)
Age 49 (39, 59) 42 (33, 50) 50 (40, 59) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 97 (2.7%) 14 (4.0%) 83 (2.5%)
    ≥25-<35 457 (13%) 89 (25%) 368 (11%)
    ≥35-<45 814 (22%) 115 (33%) 699 (21%)
    ≥45-<55 968 (27%) 85 (24%) 883 (27%)
    ≥55-<80 1,245 (34%) 48 (14%) 1,197 (37%)
    ≥80 45 (1.2%) 2 (0.6%) 43 (1.3%)
WHO region (origin)



    WHO Africa 635 (19%) 15 (4.4%) 620 (20%)
    WHO Americas 94 (2.8%) 7 (2.1%) 87 (2.8%)
    WHO Eastern Mediterranean 106 (3.1%) 5 (1.5%) 101 (3.3%)
    WHO Europe 2,541 (74%) 312 (92%) 2,229 (73%)
    WHO South-East Asia 16 (0.5%) 0 (0%) 16 (0.5%)
    WHO Western Pacific 20 (0.6%) 0 (0%) 20 (0.7%)
HIV stage



    A 1 (<0.1%) 0 (0%) 1 (<0.1%)
    A0 2 (<0.1%) 1 (0.3%) 1 (<0.1%)
    A1 480 (13%) 88 (25%) 392 (12%)
    A2 1,225 (34%) 171 (48%) 1,054 (32%)
    A3 704 (19%) 49 (14%) 655 (20%)
    B 1 (<0.1%) 0 (0%) 1 (<0.1%)
    B0 4 (0.1%) 0 (0%) 4 (0.1%)
    B1 35 (1.0%) 7 (2.0%) 28 (0.9%)
    B2 141 (3.9%) 10 (2.8%) 131 (4.0%)
    B3 227 (6.3%) 4 (1.1%) 223 (6.8%)
    C 10 (0.3%) 0 (0%) 10 (0.3%)
    C0 2 (<0.1%) 0 (0%) 2 (<0.1%)
    C1 16 (0.4%) 1 (0.3%) 15 (0.5%)
    C2 119 (3.3%) 4 (1.1%) 115 (3.5%)
    C3 659 (18%) 18 (5.1%) 641 (20%)
Primo-infection


<0.001
    Non 3,194 (88%) 254 (72%) 2,940 (90%)
    Oui 432 (12%) 99 (28%) 333 (10%)
Transmission risk



    Bisexual 168 (4.6%) 15 (4.2%) 153 (4.7%)
    Blood 61 (1.7%) 1 (0.3%) 60 (1.8%)
    Heterosexual 1,203 (33%) 30 (8.5%) 1,173 (36%)
    IDU 199 (5.5%) 4 (1.1%) 195 (6.0%)
    Mother to child transmission 52 (1.4%) 0 (0%) 52 (1.6%)
    MSM 1,653 (46%) 286 (81%) 1,367 (42%)
    Others 29 (0.8%) 3 (0.8%) 26 (0.8%)
    Unknown 261 (7.2%) 14 (4.0%) 247 (7.5%)
Drug use



    Current 328 (11%) 53 (17%) 275 (9.8%)
    None 1,923 (62%) 167 (53%) 1,756 (63%)
    Past 351 (11%) 25 (7.9%) 326 (12%)
    Sometimes 296 (9.5%) 60 (19%) 236 (8.4%)
    Substitution 45 (1.4%) 2 (0.6%) 43 (1.5%)
    Unknown 174 (5.6%) 10 (3.2%) 164 (5.9%)
Baseline HIV RNA level (log10) 4.92 (4.27, 5.59) 5.08 (4.55, 5.80) 4.89 (4.22, 5.57) <0.001
Baseline CD4 count 392 (202, 581) 473 (334, 665) 366 (178, 565) <0.001
1 n (%); Median (IQR)
2 Fisher’s exact test; Wilcoxon rank sum test; Pearson’s Chi-squared test

Cluster growth

Top growing clusters

New entries

Bretagne

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 50/1,256, i.e. 4%.

Cluster size and composition

Overall

By origin

Demographics by clustering status

Characteristic Overall, N = 1,2561 Clusters size ≥3, N = 501 Singletons, N = 1,2061 p-value2
sex


<0.001
    Female 428 (34%) 4 (8.0%) 424 (35%)
    Male 822 (65%) 45 (90%) 777 (64%)
    Transgender F/M 1 (<0.1%) 0 (0%) 1 (<0.1%)
    Transgender M/F 5 (0.4%) 1 (2.0%) 4 (0.3%)
Age 52 (41, 60) 48 (38, 59) 52 (42, 60) 0.2
Age group


0.5
    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 38 (3.0%) 1 (2.0%) 37 (3.1%)
    ≥25-<35 129 (10%) 8 (16%) 121 (10%)
    ≥35-<45 245 (20%) 13 (26%) 232 (19%)
    ≥45-<55 310 (25%) 11 (22%) 299 (25%)
    ≥55-<80 518 (41%) 17 (34%) 501 (42%)
    ≥80 16 (1.3%) 0 (0%) 16 (1.3%)
WHO region (origin)


<0.001
    WHO Africa 290 (24%) 0 (0%) 290 (25%)
    WHO Americas 33 (2.7%) 0 (0%) 33 (2.8%)
    WHO Eastern Mediterranean 9 (0.7%) 0 (0%) 9 (0.8%)
    WHO Europe 887 (72%) 49 (100%) 838 (71%)
    WHO South-East Asia 3 (0.2%) 0 (0%) 3 (0.3%)
    WHO Western Pacific 7 (0.6%) 0 (0%) 7 (0.6%)
HIV stage



    A 2 (0.2%) 0 (0%) 2 (0.2%)
    A0 1 (<0.1%) 0 (0%) 1 (<0.1%)
    A1 134 (11%) 11 (22%) 123 (10%)
    A2 365 (29%) 18 (36%) 347 (29%)
    A3 233 (19%) 8 (16%) 225 (19%)
    B0 11 (0.9%) 0 (0%) 11 (0.9%)
    B1 9 (0.7%) 0 (0%) 9 (0.7%)
    B2 71 (5.7%) 2 (4.0%) 69 (5.7%)
    B3 101 (8.0%) 0 (0%) 101 (8.4%)
    C 14 (1.1%) 2 (4.0%) 12 (1.0%)
    C0 2 (0.2%) 0 (0%) 2 (0.2%)
    C1 2 (0.2%) 0 (0%) 2 (0.2%)
    C2 36 (2.9%) 1 (2.0%) 35 (2.9%)
    C3 275 (22%) 8 (16%) 267 (22%)
Primo-infection


<0.001
    Non 1,183 (94%) 40 (80%) 1,143 (95%)
    Oui 73 (5.8%) 10 (20%) 63 (5.2%)
Transmission risk



    Bisexual 58 (4.6%) 10 (20%) 48 (4.0%)
    Blood 27 (2.1%) 1 (2.0%) 26 (2.2%)
    Heterosexual 563 (45%) 5 (10%) 558 (46%)
    IDU 72 (5.7%) 3 (6.0%) 69 (5.7%)
    Mother to child transmission 27 (2.1%) 0 (0%) 27 (2.2%)
    MSM 438 (35%) 30 (60%) 408 (34%)
    Others 15 (1.2%) 0 (0%) 15 (1.2%)
    Unknown 56 (4.5%) 1 (2.0%) 55 (4.6%)
Drug use


0.032
    Current 90 (9.0%) 8 (20%) 82 (8.6%)
    None 425 (43%) 19 (46%) 406 (43%)
    Past 74 (7.4%) 0 (0%) 74 (7.8%)
    Sometimes 23 (2.3%) 1 (2.4%) 22 (2.3%)
    Substitution 22 (2.2%) 2 (4.9%) 20 (2.1%)
    Unknown 361 (36%) 11 (27%) 350 (37%)
Baseline HIV RNA level (log10) 4.87 (4.14, 5.48) 5.07 (4.16, 5.62) 4.86 (4.14, 5.48) 0.5
Baseline CD4 count 353 (180, 547) 423 (253, 595) 351 (175, 543) 0.2
1 n (%); Median (IQR)
2 Fisher’s exact test; Wilcoxon rank sum test

Cluster growth

Top growing clusters

New entries

Provence-Alpes-Côte-d’Azur

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 256/2,787, i.e. 9%.

Cluster size and composition

Overall

By origin

Demographics by clustering status

Characteristic Overall, N = 2,7871 Clusters size ≥3, N = 2561 Singletons, N = 2,5311 p-value2
sex


<0.001
    Female 728 (26%) 18 (7.0%) 710 (28%)
    Male 2,005 (72%) 234 (91%) 1,771 (70%)
    Transgender M/F 54 (1.9%) 4 (1.6%) 50 (2.0%)
Age 52 (41, 60) 42 (34, 52) 53 (42, 60) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 59 (2.1%) 16 (6.3%) 43 (1.7%)
    ≥25-<35 307 (11%) 53 (21%) 254 (10%)
    ≥35-<45 545 (20%) 79 (31%) 466 (18%)
    ≥45-<55 671 (24%) 55 (21%) 616 (24%)
    ≥55-<80 1,179 (42%) 52 (20%) 1,127 (45%)
    ≥80 26 (0.9%) 1 (0.4%) 25 (1.0%)
WHO region (origin)



    WHO Africa 308 (16%) 8 (4.0%) 300 (17%)
    WHO Americas 118 (6.1%) 7 (3.5%) 111 (6.4%)
    WHO Eastern Mediterranean 89 (4.6%) 5 (2.5%) 84 (4.9%)
    WHO Europe 1,382 (72%) 178 (89%) 1,204 (70%)
    WHO South-East Asia 7 (0.4%) 1 (0.5%) 6 (0.3%)
    WHO Western Pacific 18 (0.9%) 0 (0%) 18 (1.0%)
HIV stage



    A 2 (<0.1%) 0 (0%) 2 (<0.1%)
    A0 20 (0.7%) 2 (0.8%) 18 (0.7%)
    A1 390 (14%) 83 (32%) 307 (12%)
    A2 983 (35%) 126 (49%) 857 (34%)
    A3 442 (16%) 20 (7.8%) 422 (17%)
    B0 2 (<0.1%) 0 (0%) 2 (<0.1%)
    B1 23 (0.8%) 2 (0.8%) 21 (0.8%)
    B2 118 (4.2%) 5 (2.0%) 113 (4.5%)
    B3 187 (6.7%) 3 (1.2%) 184 (7.3%)
    C 1 (<0.1%) 0 (0%) 1 (<0.1%)
    C0 3 (0.1%) 0 (0%) 3 (0.1%)
    C1 22 (0.8%) 0 (0%) 22 (0.9%)
    C2 107 (3.8%) 6 (2.3%) 101 (4.0%)
    C3 487 (17%) 9 (3.5%) 478 (19%)
Primo-infection


<0.001
    Non 2,555 (92%) 205 (80%) 2,350 (93%)
    Oui 232 (8.3%) 51 (20%) 181 (7.2%)
Transmission risk



    Bisexual 123 (4.4%) 18 (7.0%) 105 (4.1%)
    Blood 44 (1.6%) 0 (0%) 44 (1.7%)
    Heterosexual 992 (36%) 46 (18%) 946 (37%)
    IDU 392 (14%) 11 (4.3%) 381 (15%)
    Mother to child transmission 51 (1.8%) 0 (0%) 51 (2.0%)
    MSM 1,109 (40%) 179 (70%) 930 (37%)
    Others 11 (0.4%) 0 (0%) 11 (0.4%)
    Unknown 65 (2.3%) 2 (0.8%) 63 (2.5%)
Drug use



    Current 300 (11%) 46 (18%) 254 (10%)
    None 788 (29%) 68 (27%) 720 (29%)
    Past 335 (12%) 38 (15%) 297 (12%)
    Sometimes 33 (1.2%) 3 (1.2%) 30 (1.2%)
    Substitution 55 (2.0%) 0 (0%) 55 (2.2%)
    Unknown 1,215 (45%) 97 (38%) 1,118 (45%)
Baseline HIV RNA level (log10) 4.81 (4.08, 5.46) 4.90 (4.21, 5.43) 4.81 (4.04, 5.46) 0.082
Baseline CD4 count 410 (247, 591) 510 (357, 696) 390 (221, 567) <0.001
1 n (%); Median (IQR)
2 Fisher’s exact test; Wilcoxon rank sum test; Pearson’s Chi-squared test

Cluster growth

Top growing clusters

New entries

Normandie

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 28/690, i.e. 4%.

Cluster size and composition

Overall

By origin

Demographics by clustering status

Characteristic Overall, N = 6901 Clusters size ≥3, N = 281 Singletons, N = 6621 p-value2
sex


<0.001
    Female 242 (35%) 1 (3.6%) 241 (36%)
    Male 431 (62%) 27 (96%) 404 (61%)
    Transgender F/M 1 (0.1%) 0 (0%) 1 (0.2%)
    Transgender M/F 16 (2.3%) 0 (0%) 16 (2.4%)
Age 49 (38, 58) 48 (33, 53) 49 (38, 58) 0.067
Age group


0.011
    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 21 (3.0%) 4 (14%) 17 (2.6%)
    ≥25-<35 107 (16%) 4 (14%) 103 (16%)
    ≥35-<45 148 (21%) 5 (18%) 143 (22%)
    ≥45-<55 174 (25%) 11 (39%) 163 (25%)
    ≥55-<80 233 (34%) 4 (14%) 229 (35%)
    ≥80 7 (1.0%) 0 (0%) 7 (1.1%)
WHO region (origin)


0.032
    WHO Africa 206 (31%) 2 (7.4%) 204 (32%)
    WHO Americas 36 (5.4%) 0 (0%) 36 (5.6%)
    WHO Eastern Mediterranean 6 (0.9%) 0 (0%) 6 (0.9%)
    WHO Europe 419 (62%) 25 (93%) 394 (61%)
    WHO South-East Asia 3 (0.4%) 0 (0%) 3 (0.5%)
    WHO Western Pacific 1 (0.1%) 0 (0%) 1 (0.2%)
HIV stage



    A1 102 (15%) 11 (39%) 91 (14%)
    A2 219 (32%) 14 (50%) 205 (31%)
    A3 102 (15%) 1 (3.6%) 101 (15%)
    B 1 (0.1%) 0 (0%) 1 (0.2%)
    B1 9 (1.3%) 0 (0%) 9 (1.4%)
    B2 39 (5.7%) 1 (3.6%) 38 (5.7%)
    B3 52 (7.5%) 0 (0%) 52 (7.9%)
    C 1 (0.1%) 0 (0%) 1 (0.2%)
    C0 1 (0.1%) 0 (0%) 1 (0.2%)
    C1 2 (0.3%) 0 (0%) 2 (0.3%)
    C2 23 (3.3%) 0 (0%) 23 (3.5%)
    C3 139 (20%) 1 (3.6%) 138 (21%)
Primo-infection


0.002
    Non 578 (84%) 17 (61%) 561 (85%)
    Oui 112 (16%) 11 (39%) 101 (15%)
Transmission risk


0.2
    Bisexual 45 (6.5%) 5 (18%) 40 (6.0%)
    Blood 11 (1.6%) 0 (0%) 11 (1.7%)
    Heterosexual 356 (52%) 9 (32%) 347 (52%)
    IDU 39 (5.7%) 1 (3.6%) 38 (5.7%)
    Mother to child transmission 8 (1.2%) 0 (0%) 8 (1.2%)
    MSM 203 (29%) 12 (43%) 191 (29%)
    Others 6 (0.9%) 0 (0%) 6 (0.9%)
    Unknown 22 (3.2%) 1 (3.6%) 21 (3.2%)
Drug use


0.029
    Current 51 (11%) 5 (22%) 46 (10%)
    None 309 (65%) 11 (48%) 298 (65%)
    Past 47 (9.8%) 6 (26%) 41 (9.0%)
    Sometimes 18 (3.8%) 1 (4.3%) 17 (3.7%)
    Substitution 21 (4.4%) 0 (0%) 21 (4.6%)
    Unknown 33 (6.9%) 0 (0%) 33 (7.2%)
Baseline HIV RNA level (log10) 4.78 (3.88, 5.53) 5.34 (4.44, 6.16) 4.76 (3.84, 5.51) 0.011
Baseline CD4 count 353 (180, 574) 503 (361, 648) 340 (175, 569) 0.005
1 n (%); Median (IQR)
2 Fisher’s exact test; Wilcoxon rank sum test

Cluster growth

Top growing clusters

New entries

Guadeloupe

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 37/645, i.e. 6%.

Cluster size and composition

Overall

By origin

Demographics by clustering status

Characteristic Overall, N = 6451 Clusters size ≥3, N = 371 Singletons, N = 6081 p-value2
sex


<0.001
    Female 240 (37%) 2 (5.4%) 238 (39%)
    Male 405 (63%) 35 (95%) 370 (61%)
Age 50 (38, 60) 34 (28, 45) 50 (40, 60) <0.001
Age group


<0.001
    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 29 (4.5%) 5 (14%) 24 (3.9%)
    ≥25-<35 100 (16%) 16 (43%) 84 (14%)
    ≥35-<45 110 (17%) 5 (14%) 105 (17%)
    ≥45-<55 169 (26%) 7 (19%) 162 (27%)
    ≥55-<80 223 (35%) 4 (11%) 219 (36%)
    ≥80 14 (2.2%) 0 (0%) 14 (2.3%)
WHO region (origin)


0.011
    WHO Africa 4 (0.6%) 0 (0%) 4 (0.7%)
    WHO Americas 232 (36%) 4 (11%) 228 (38%)
    WHO Eastern Mediterranean 2 (0.3%) 0 (0%) 2 (0.3%)
    WHO Europe 399 (62%) 33 (89%) 366 (61%)
    WHO South-East Asia 1 (0.2%) 0 (0%) 1 (0.2%)
    WHO Western Pacific 1 (0.2%) 0 (0%) 1 (0.2%)
HIV stage



    A 2 (0.3%) 1 (2.7%) 1 (0.2%)
    A0 1 (0.2%) 0 (0%) 1 (0.2%)
    A1 66 (10%) 9 (24%) 57 (9.4%)
    A2 204 (32%) 19 (51%) 185 (30%)
    A3 114 (18%) 2 (5.4%) 112 (18%)
    B1 6 (0.9%) 0 (0%) 6 (1.0%)
    B2 17 (2.6%) 0 (0%) 17 (2.8%)
    B3 38 (5.9%) 2 (5.4%) 36 (5.9%)
    C 1 (0.2%) 0 (0%) 1 (0.2%)
    C1 3 (0.5%) 1 (2.7%) 2 (0.3%)
    C2 12 (1.9%) 0 (0%) 12 (2.0%)
    C3 181 (28%) 3 (8.1%) 178 (29%)
Primo-infection


0.004
    Non 616 (96%) 31 (84%) 585 (96%)
    Oui 29 (4.5%) 6 (16%) 23 (3.8%)
Transmission risk


<0.001
    Bisexual 41 (6.4%) 4 (11%) 37 (6.1%)
    Blood 5 (0.8%) 0 (0%) 5 (0.8%)
    Heterosexual 470 (73%) 15 (41%) 455 (75%)
    IDU 7 (1.1%) 0 (0%) 7 (1.2%)
    Mother to child transmission 6 (0.9%) 0 (0%) 6 (1.0%)
    MSM 101 (16%) 17 (46%) 84 (14%)
    Others 1 (0.2%) 0 (0%) 1 (0.2%)
    Unknown 14 (2.2%) 1 (2.7%) 13 (2.1%)
Drug use


0.065
    Current 44 (7.8%) 6 (19%) 38 (7.1%)
    None 425 (75%) 23 (72%) 402 (75%)
    Past 45 (8.0%) 0 (0%) 45 (8.4%)
    Sometimes 17 (3.0%) 2 (6.3%) 15 (2.8%)
    Substitution 2 (0.4%) 0 (0%) 2 (0.4%)
    Unknown 32 (5.7%) 1 (3.1%) 31 (5.8%)
Baseline HIV RNA level (log10) 4.67 (4.07, 5.16) 4.64 (4.16, 4.95) 4.67 (4.07, 5.18) 0.8
Baseline CD4 count 332 (149, 494) 394 (301, 557) 327 (140, 491) 0.052
1 n (%); Median (IQR)
2 Pearson’s Chi-squared test; Wilcoxon rank sum test; Fisher’s exact test

Cluster growth

Top growing clusters

New entries

Auvergne-Rhône-Alpes

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 8/303, i.e. 3%.

Cluster size and composition

Overall

By origin

Demographics by clustering status

Characteristic Overall, N = 3031 Clusters size ≥3, N = 81 Singletons, N = 2951 p-value2
sex


0.082
    Female 98 (32%) 0 (0%) 98 (33%)
    Male 204 (67%) 8 (100%) 196 (66%)
    Transgender M/F 1 (0.3%) 0 (0%) 1 (0.3%)
Age 49 (38, 58) 52 (44, 54) 48 (38, 58) 0.7
Age group


0.6
    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 4 (1.3%) 0 (0%) 4 (1.4%)
    ≥25-<35 47 (16%) 0 (0%) 47 (16%)
    ≥35-<45 75 (25%) 2 (25%) 73 (25%)
    ≥45-<55 77 (25%) 4 (50%) 73 (25%)
    ≥55-<80 95 (31%) 2 (25%) 93 (32%)
    ≥80 5 (1.7%) 0 (0%) 5 (1.7%)
WHO region (origin)


0.5
    WHO Africa 65 (22%) 0 (0%) 65 (23%)
    WHO Americas 9 (3.1%) 0 (0%) 9 (3.2%)
    WHO Eastern Mediterranean 5 (1.7%) 0 (0%) 5 (1.8%)
    WHO Europe 209 (72%) 8 (100%) 201 (71%)
    WHO South-East Asia 1 (0.3%) 0 (0%) 1 (0.4%)
    WHO Western Pacific 2 (0.7%) 0 (0%) 2 (0.7%)
HIV stage


0.2
    A1 48 (16%) 4 (50%) 44 (15%)
    A2 97 (32%) 4 (50%) 93 (32%)
    A3 52 (17%) 0 (0%) 52 (18%)
    B1 2 (0.7%) 0 (0%) 2 (0.7%)
    B2 15 (5.0%) 0 (0%) 15 (5.1%)
    B3 24 (7.9%) 0 (0%) 24 (8.1%)
    C1 3 (1.0%) 0 (0%) 3 (1.0%)
    C2 6 (2.0%) 0 (0%) 6 (2.0%)
    C3 56 (18%) 0 (0%) 56 (19%)
Primo-infection


0.12
    Non 255 (84%) 5 (63%) 250 (85%)
    Oui 48 (16%) 3 (38%) 45 (15%)
Transmission risk


0.090
    Bisexual 24 (7.9%) 2 (25%) 22 (7.5%)
    Blood 6 (2.0%) 0 (0%) 6 (2.0%)
    Heterosexual 127 (42%) 0 (0%) 127 (43%)
    IDU 8 (2.6%) 0 (0%) 8 (2.7%)
    Mother to child transmission 9 (3.0%) 0 (0%) 9 (3.1%)
    MSM 117 (39%) 6 (75%) 111 (38%)
    Others 1 (0.3%) 0 (0%) 1 (0.3%)
    Unknown 11 (3.6%) 0 (0%) 11 (3.7%)
Drug use


0.7
    Current 40 (14%) 2 (25%) 38 (14%)
    None 190 (66%) 6 (75%) 184 (66%)
    Past 36 (13%) 0 (0%) 36 (13%)
    Sometimes 8 (2.8%) 0 (0%) 8 (2.9%)
    Substitution 4 (1.4%) 0 (0%) 4 (1.4%)
    Unknown 10 (3.5%) 0 (0%) 10 (3.6%)
Baseline HIV RNA level (log10) 4.65 (3.98, 5.26) 5.26 (4.41, 6.03) 4.64 (3.97, 5.25) 0.2
Baseline CD4 count 442 (271, 638) 601 (538, 657) 436 (269, 634) 0.2
1 n (%); Median (IQR)
2 Fisher’s exact test; Wilcoxon rank sum test

Cluster growth

Top growing clusters

New entries

Martinique

Sampling

Clustering rate

The overall clustering rate with a genetic distance threshold of 0.5% is 94/922, i.e. 10%.

Cluster size and composition

Overall

By origin

Demographics by clustering status

Characteristic Overall, N = 9221 Clusters size ≥3, N = 941 Singletons, N = 8281 p-value2
sex


0.4
    Female 318 (34%) 27 (29%) 291 (35%)
    Male 599 (65%) 67 (71%) 532 (64%)
    Transgender M/F 5 (0.5%) 0 (0%) 5 (0.6%)
Age 53 (40, 63) 37 (30, 52) 55 (42, 63) <0.001
Age group



    <15 0 (0%) 0 (0%) 0 (0%)
    ≥15-<25 32 (3.5%) 9 (9.6%) 23 (2.8%)
    ≥25-<35 123 (13%) 33 (35%) 90 (11%)
    ≥35-<45 145 (16%) 17 (18%) 128 (15%)
    ≥45-<55 182 (20%) 14 (15%) 168 (20%)
    ≥55-<80 413 (45%) 21 (22%) 392 (47%)
    ≥80 27 (2.9%) 0 (0%) 27 (3.3%)
WHO region (origin)


0.013
    WHO Africa 13 (1.5%) 0 (0%) 13 (1.6%)
    WHO Americas 121 (14%) 5 (5.6%) 116 (15%)
    WHO Eastern Mediterranean 2 (0.2%) 1 (1.1%) 1 (0.1%)
    WHO Europe 751 (85%) 84 (93%) 667 (84%)
HIV stage



    A0 1 (0.1%) 0 (0%) 1 (0.1%)
    A1 96 (10%) 20 (21%) 76 (9.2%)
    A2 277 (30%) 39 (41%) 238 (29%)
    A3 167 (18%) 18 (19%) 149 (18%)
    B1 5 (0.5%) 0 (0%) 5 (0.6%)
    B2 39 (4.2%) 3 (3.2%) 36 (4.3%)
    B3 63 (6.8%) 2 (2.1%) 61 (7.4%)
    C0 1 (0.1%) 0 (0%) 1 (0.1%)
    C1 2 (0.2%) 2 (2.1%) 0 (0%)
    C2 19 (2.1%) 1 (1.1%) 18 (2.2%)
    C3 252 (27%) 9 (9.6%) 243 (29%)
Primo-infection


<0.001
    Non 851 (92%) 77 (82%) 774 (93%)
    Oui 71 (7.7%) 17 (18%) 54 (6.5%)
Transmission risk


0.041
    Bisexual 126 (14%) 22 (23%) 104 (13%)
    Blood 9 (1.0%) 1 (1.1%) 8 (1.0%)
    Heterosexual 588 (64%) 47 (50%) 541 (65%)
    IDU 14 (1.5%) 1 (1.1%) 13 (1.6%)
    Mother to child transmission 3 (0.3%) 0 (0%) 3 (0.4%)
    MSM 169 (18%) 23 (24%) 146 (18%)
    Others 1 (0.1%) 0 (0%) 1 (0.1%)
    Unknown 12 (1.3%) 0 (0%) 12 (1.4%)
Drug use


0.041
    Current 108 (13%) 18 (21%) 90 (12%)
    None 595 (70%) 50 (59%) 545 (71%)
    Past 124 (14%) 13 (15%) 111 (14%)
    Sometimes 16 (1.9%) 4 (4.7%) 12 (1.6%)
    Substitution 4 (0.5%) 0 (0%) 4 (0.5%)
    Unknown 9 (1.1%) 0 (0%) 9 (1.2%)
Baseline HIV RNA level (log10) 4.53 (3.94, 5.10) 4.36 (4.04, 4.94) 4.54 (3.93, 5.12) 0.3
Baseline CD4 count 393 (208, 571) 441 (320, 626) 385 (191, 562) 0.005
1 n (%); Median (IQR)
2 Fisher’s exact test; Wilcoxon rank sum test; Pearson’s Chi-squared test

Cluster growth

Top growing clusters

New entries